YrhK - PFAM28P - GREMLIN Contacts

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YrhK - YrhK-like protein

PFAM:	PF14145	Sequences: RRYEALSTANDALGSICFLVGSVLFFAEVCHRWSWWIAGTWLFLLGSVLFGISAVARLVRPI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	62 (58)
Sequences:	2411 (1448)
Seq/√Len:	190.2
META:	0.778

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
22_S	47_S	4.210	1.00
26_F	44_L	2.493	1.00
19_L	44_L	2.158	1.00
24_L	35_W	2.100	1.00
36_W	40_T	1.938	1.00
35_W	38_A	1.719	1.00
44_L	48_V	1.699	1.00
12_A	51_G	1.657	1.00
17_C	49_L	1.651	1.00
25_F	43_F	1.616	1.00
7_S	53_S	1.540	1.00
15_S	50_F	1.524	1.00
19_L	48_V	1.471	1.00
21_G	25_F	1.469	1.00
12_A	55_V	1.451	1.00
26_F	41_W	1.442	1.00
14_G	50_F	1.384	1.00
17_C	42_L	1.374	1.00
18_F	47_S	1.256	1.00
29_V	34_S	1.194	1.00
4_E	57_R	1.180	1.00
28_E	31_H	1.148	1.00
32_R	35_W	1.108	1.00
29_V	33_W	1.090	1.00
36_W	39_G	1.070	1.00
27_A	30_C	1.045	1.00
34_S	38_A	1.042	1.00
30_C	33_W	1.032	1.00
11_D	53_S	1.018	1.00
23_V	27_A	1.010	1.00
53_S	56_A	1.008	1.00
50_F	53_S	1.001	1.00
23_V	30_C	0.995	0.99
38_A	42_L	0.972	0.99
21_G	47_S	0.972	0.99
14_G	49_L	0.967	0.99
30_C	34_S	0.949	0.99
37_I	40_T	0.923	0.99
4_E	60_R	0.905	0.99
3_Y	7_S	0.895	0.99
23_V	44_L	0.893	0.99
25_F	39_G	0.846	0.98
23_V	32_R	0.832	0.98
21_G	27_A	0.829	0.98
11_D	54_A	0.816	0.98
35_W	39_G	0.803	0.98
50_F	54_A	0.797	0.98
15_S	51_G	0.791	0.97
18_F	50_F	0.782	0.97
13_L	17_C	0.774	0.97
4_E	8_T	0.748	0.96
7_S	57_R	0.732	0.96
11_D	50_F	0.730	0.96
22_S	25_F	0.728	0.96
10_N	49_L	0.721	0.96
3_Y	11_D	0.702	0.95
5_A	8_T	0.695	0.95
14_G	53_S	0.694	0.95
11_D	15_S	0.689	0.94
53_S	57_R	0.687	0.94
4_E	7_S	0.685	0.94
33_W	36_W	0.677	0.94
13_L	49_L	0.673	0.94
39_G	50_F	0.659	0.93
34_S	37_I	0.649	0.92
48_V	52_I	0.648	0.92
21_G	24_L	0.638	0.92
13_L	16_I	0.629	0.91
52_I	55_V	0.626	0.91
5_A	9_A	0.618	0.90
15_S	54_A	0.617	0.90
18_F	41_W	0.611	0.90
5_A	48_V	0.607	0.90
49_L	52_I	0.601	0.89
12_A	50_F	0.592	0.88
27_A	31_H	0.591	0.88
21_G	43_F	0.579	0.87
5_A	17_C	0.561	0.86
11_D	14_G	0.559	0.85
21_G	39_G	0.552	0.85
12_A	60_R	0.549	0.84
7_S	10_N	0.538	0.83
43_F	47_S	0.535	0.83
29_V	38_A	0.519	0.81
9_A	48_V	0.515	0.80
54_A	57_R	0.508	0.80
23_V	28_E	0.500	0.78

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
3wxwA	1	0.9355	7.5	0.839	Contact Map
1v54A	1	0.629	4.4	0.855	Contact Map
3wfdB	1	0.4839	4	0.858	Contact Map
4x5mA	2	0.871	2.5	0.873	Contact Map
1eysM	1	1	2.5	0.873	Contact Map
1fftA	1	1	2.4	0.873	Contact Map
2wjnM	1	1	2.4	0.874	Contact Map
1eysL	1	1	2.3	0.874	Contact Map
4p79A	1	1	2.3	0.875	Contact Map
1vryA	1	0.871	2.1	0.877	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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